The PV is done based on intensities. For each voxel an the boundary of an ROI, the voxel intensity is assumed to be a weighted summation of the the average intensities in each ROI. Knowing the average intensities in the ROIs and the actual intensity of the voxel, the PV can be computed. doug
On 12/17/2012 09:59 AM, Gabriel Gonzalez Escamilla wrote: > Thanks Doug, > > In my case I did as you said but as Bruce recommend use the wmparc, so > the voxels less than 4000, and = 5001 were left , and more than or > equal to 4000, and =5002 were right. > > So different approach but I think would be the same, isn't it? > > Can you explain to me how FS makes the PV correction on the output > volumes in aseg.stats? > > > Best Regards, > Gabriel. > > > El 13/12/12, *Douglas N Greve * <gr...@nmr.mgh.harvard.edu> escribió: >> >> Gabriel, the way I've done it is to just assign WMSA to left or right >> based on the column number of the WMSA voxel. If it is less than 128, >> then it is right (78) if it is greater than 128 it is left (79). It's >> not perfect, but it is correct in the vast majority of cases. >> doug >> >> >> On 12/12/2012 01:56 PM, Gabriel Gonzalez Escamilla wrote: >> >Thanks Bruce, >> > >> >The problem is that for this set of subjects I only have the T1s, >> anyways I would like to give a try onto the tools for WMSA, since I >> have T2 from some subjects. >> > >> >On the other hand, If I'm right the way to do the assignment on >> matlab, would be something like opening the mgz, finding their >> positions and look which are the neighbors right? >> >If so, I would like to not assign just the neighbor voxel, as this >> might bias the assignment, I'm guessing that something like the >> assignment done during the aparc+aseg.mgz creation (using GM >> parcelation to map GM labels to the wm voxels - mri_aparc2aseg) >> should be a correct way to do so. Can you point me to an article or >> explain to me how this works indeed, and how the decision to the >> belonging voxel is made, I think I know the basis, but not enough to >> make my own script. >> > >> >If I do not understand bad, is something like, you take a voxel a >> look to some contiguous voxels till you get into a point where all >> the contiguous voxels are too far from the seed, and are surrounded >> by lots of voxels belonging to other areas. I'm not quite sure about >> the decision about when to stop the search. I really think that the >> method like the implemented in the mri_apar2aseg is the perfect solution. >> > >> >Regards, >> >Gabriel >> > >> > >> > >> > >> >El 12/12/12, *Bruce Fischl * <fis...@nmr.mgh.harvard.edu> escribió: >> >>then I would either use TRACULA (if you have DWI) or the wmparc to >> generate ROIs. I meant that you could count whether there are more lh >> or rh wm labels neighboring each one to figure out which hemi they are in >> >> >> >>cheers >> >>Bruce >> >> >> >> >> >>On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: >> >> >> >>>Yes I did loo at the total WH-hypointensities(77), and substract >> them without a problem. >> >>> >> >>>What do you mean with lateralize them based on neighboring labels? >> How can I perform such thing on FS? >> >>> >> >>>Actually I'm interested in knowing to wich specific label o region >> they are. >> >>> >> >>>Bests, >> >>>Gabriel >> >>> >> >>> >> >>>El 12/12/12, Bruce Fischl <fis...@nmr.mgh.harvard.edu> escribió: >> >>> Hi Gabriel >> >>> >> >>> we don't lateralize them by default, so look for >> WM_hypointensities (77) instead. It would be pretty easy to >> >>> lateralize them based on neighboring labels. >> >>> >> >>> cheers >> >>> Bruce >> >>> >> >>> >> >>> On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: >> >>> >> >>> > >> >>> >Dear Freesurfers, >> >>> > >> >>> >I'm looking for a way to compute the left and right >> WM-hypointensities, as volume values or images. They always >> >>> appear empty in >> >>> >the aseg.stats, and the corresponding segs No 78 & 79 do >> not appear in the aseg.mgz, and I'm a bit lost with it. >> >>> > >> >>> >Can any one help me? >> >>> > >> >>> >Best Regards, >> >>> >Gabriel. >> >>> > >> >>> > >> >>> >> >>> >> >>> The information in this e-mail is intended only for the >> person to whom it is >> >>> addressed. If you believe this e-mail was sent to you in >> error and the e-mail >> >>> contains patient information, please contact the Partners >> Compliance HelpLine at >> >>> http://www.partners.org/complianceline . If the e-mail was sent >> to you in error >> >>> but does not contain patient information, please contact the >> sender and properly >> >>> dispose of the e-mail. >> >>> >> >>> >> >>>-- >> >>>-------------------------- >> >>>PhD. student Gabriel González-Escamilla >> >>>Laboratory of Functional Neuroscience >> >>>Department of Physiology, Anatomy, and Cell Biology >> >>>University Pablo de Olavide >> >>>Ctra. de Utrera, Km.1 >> >>>41013 - Seville >> >>>- Spain - >> >>> >> >>>Email: ggon...@upo.es >> >>>http://www.upo.es/neuroaging/es/ >> >>> >> > >> >-- >> >-------------------------- >> >PhD. student Gabriel González-Escamilla >> >Laboratory of Functional Neuroscience >> >Department of Physiology, Anatomy, and Cell Biology >> >University Pablo de Olavide >> >Ctra. de Utrera, Km.1 >> >41013 - Seville >> >- Spain - >> > >> >Email: ggon...@upo.es >> >http://www.upo.es/neuroaging/es/ >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > > -- > -------------------------- > PhD. student Gabriel González-Escamilla > Laboratory of Functional Neuroscience > Department of Physiology, Anatomy, and Cell Biology > University Pablo de Olavide > Ctra. de Utrera, Km.1 > 41013 - Seville > - Spain - > > Email: ggon...@upo.es > http://www.upo.es/neuroaging/es/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
